Welcome to the forums, reverend! :-)
In addition to the tip from Hypotyposis, I wanted to mention the
Perspectives -> All Items
menu item as a quick way to double-check that the items in question are still in the database.
That menu item sets all your view settings to the most permissive options; at that point, you can use the Search field to find items by name. Even if they've been accidentally checked off or moved to some other place in the database.
If that doesn't help find your items, feel free to contact the support ninjas via email (
omnifocus@omnigroup.com) or phone (800.315.6664) and we'll be happy to assist!